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A Transcriptomic Biomarker to Classify Chemical-Induced Histone Deacetylase Inhibition in Human HepaRG Cells

GSE342302 Homo sapiens (human) RNA-seq (gene expression) 477 samples Submitted 2026/08/04 Platform GPL18573Platform GPL30173
At a glance

RNA-seq (gene expression) · human · 477 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Homo sapiens (human)
Samples
477 samples: 78 conditions, mostly with about 4 replicates eachGroups are read from the sample names, not from the paper. Check the list below.
Data you can get
A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
This dataset
Open GSE342302 in finder → Find more human RNA-seq datasets →
Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE342302_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1507318 and SRA study SRP313167. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
78 conditions, mostly with about 4 replicates each
HCC3_ZDV_C5 ×4 HCC3_MMS_C5 ×4 HCC3_ZDV_C4 ×4 HCC3_MMS_C4 ×4 HCC3_ZDV_C3 ×4 HCC3_MMS_C3 ×4 HCC3_ZDV_C2 ×4 HCC3_MMS_C2 ×4 +162 more

Supports a between-group comparison across 308 samples.

How we read this: 78 replicated groups read from the first 400 of 477 sample titles; they account for 308 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

+ 437 more — browse all 477 samples with per-sample file links →

Datasets on a similar topic

Search all human RNA-seq datasets in GEO →

Share this dataset

Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.